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This page was generated on 2025-02-06 12:11 -0500 (Thu, 06 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4753
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4501
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4524
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4476
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4407
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1130/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.20.0  (landing page)
Lauren McIver
Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_20
git_last_commit: 1cacd4c
git_last_commit_date: 2024-10-29 10:38:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for Maaslin2 on taishan

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Maaslin2
Version: 1.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
StartedAt: 2025-02-04 08:22:58 -0000 (Tue, 04 Feb 2025)
EndedAt: 2025-02-04 08:26:16 -0000 (Tue, 04 Feb 2025)
EllapsedTime: 197.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Maaslin2_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.20.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 116.458  0.994 117.758
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in check_dep_version(dep_pkg = "TMB") :
  package version mismatch: 
glmmTMB was built with TMB package version 1.9.15
Current TMB package version is 1.9.16
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-02-04 08:25:30.268357 INFO::Writing function arguments to log file
2025-02-04 08:25:30.318912 INFO::Verifying options selected are valid
2025-02-04 08:25:30.361445 INFO::Determining format of input files
2025-02-04 08:25:30.363212 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 08:25:30.369737 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 08:25:30.371518 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2025-02-04 08:25:30.374865 INFO::Filter data based on min abundance and min prevalence
2025-02-04 08:25:30.376216 INFO::Total samples in data: 1595
2025-02-04 08:25:30.377481 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 08:25:30.385276 INFO::Total filtered features: 0
2025-02-04 08:25:30.386789 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 08:25:30.415931 INFO::Total filtered features with variance filtering: 0
2025-02-04 08:25:30.417474 INFO::Filtered feature names from variance filtering:
2025-02-04 08:25:30.418715 INFO::Running selected normalization method: TSS
2025-02-04 08:25:31.815734 INFO::Bypass z-score application to metadata
2025-02-04 08:25:31.817398 INFO::Running selected transform method: AST
2025-02-04 08:25:31.837484 INFO::Running selected analysis method: LM
2025-02-04 08:25:32.428511 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 08:25:32.876919 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 08:25:33.114014 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 08:25:33.335715 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 08:25:33.573978 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 08:25:33.804365 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 08:25:34.047612 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 08:25:34.258988 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 08:25:34.475942 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 08:25:34.74031 WARNING::Fitting problem for feature 9 a warning was issued
2025-02-04 08:25:35.026591 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 08:25:35.350217 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 08:25:35.591048 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 08:25:35.823512 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 08:25:36.046127 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 08:25:36.281268 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 08:25:36.501263 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 08:25:36.712825 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 08:25:36.934858 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 08:25:37.158423 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 08:25:37.352007 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 08:25:37.568585 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 08:25:37.796662 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 08:25:38.032968 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 08:25:38.2418 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 08:25:38.469687 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 08:25:38.701823 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 08:25:38.912181 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 08:25:39.141545 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 08:25:39.35871 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 08:25:39.579976 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 08:25:39.794668 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 08:25:40.104514 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 08:25:40.339361 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 08:25:40.576641 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 08:25:40.795006 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 08:25:40.97684 WARNING::Fitting problem for feature 35 a warning was issued
2025-02-04 08:25:41.213194 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 08:25:41.438712 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 08:25:41.653605 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 08:25:41.865744 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 08:25:42.074606 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 08:25:42.302479 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 08:25:42.532591 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 08:25:42.77775 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 08:25:42.99315 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 08:25:43.197834 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 08:25:43.423601 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 08:25:43.650801 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 08:25:43.867791 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 08:25:44.381569 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 08:25:44.596337 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 08:25:44.81572 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 08:25:45.036216 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 08:25:45.255271 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 08:25:45.484334 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 08:25:45.696657 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 08:25:45.925339 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 08:25:46.161936 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 08:25:46.389366 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 08:25:46.606775 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 08:25:46.818598 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 08:25:47.046127 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 08:25:47.248102 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 08:25:47.457838 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 08:25:47.672671 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 08:25:47.869817 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 08:25:48.069419 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 08:25:48.504849 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 08:25:48.692031 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 08:25:48.894558 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 08:25:49.124923 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 08:25:49.336652 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 08:25:49.535822 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 08:25:49.745079 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 08:25:49.938693 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 08:25:50.141217 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 08:25:50.385139 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 08:25:50.607954 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 08:25:50.831387 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 08:25:51.064878 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 08:25:51.277112 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 08:25:51.481667 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 08:25:51.711595 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 08:25:51.919614 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 08:25:52.114667 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 08:25:52.331718 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 08:25:52.53023 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 08:25:52.728496 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 08:25:53.006711 INFO::Counting total values for each feature
2025-02-04 08:25:53.055476 INFO::Writing filtered data to file output/features/filtered_data.tsv
2025-02-04 08:25:53.173923 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2025-02-04 08:25:53.293636 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2025-02-04 08:25:53.428681 INFO::Writing residuals to file output/fits/residuals.rds
2025-02-04 08:25:53.484814 INFO::Writing fitted values to file output/fits/fitted.rds
2025-02-04 08:25:53.515615 INFO::Writing extracted random effects to file output/fits/ranef.rds
2025-02-04 08:25:53.522246 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2025-02-04 08:25:53.529308 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2025-02-04 08:25:53.547375 INFO::Writing function arguments to log file
2025-02-04 08:25:53.555385 INFO::Verifying options selected are valid
2025-02-04 08:25:53.556794 INFO::Determining format of input files
2025-02-04 08:25:53.558278 INFO::Input format is data samples as rows and metadata samples as rows
2025-02-04 08:25:53.565824 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2025-02-04 08:25:53.567376 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2025-02-04 08:25:53.56961 INFO::Filter data based on min abundance and min prevalence
2025-02-04 08:25:53.570827 INFO::Total samples in data: 1595
2025-02-04 08:25:53.572006 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2025-02-04 08:25:53.580185 INFO::Total filtered features: 0
2025-02-04 08:25:53.581654 INFO::Filtered feature names from abundance and prevalence filtering:
2025-02-04 08:25:53.608304 INFO::Total filtered features with variance filtering: 0
2025-02-04 08:25:53.609772 INFO::Filtered feature names from variance filtering:
2025-02-04 08:25:53.610917 INFO::Running selected normalization method: NONE
2025-02-04 08:25:53.612077 INFO::Bypass z-score application to metadata
2025-02-04 08:25:53.613223 INFO::Running selected transform method: AST
2025-02-04 08:25:53.640182 INFO::Running selected analysis method: LM
2025-02-04 08:25:53.642465 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2025-02-04 08:25:53.840517 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2025-02-04 08:25:54.050242 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2025-02-04 08:25:54.238688 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2025-02-04 08:25:54.434265 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2025-02-04 08:25:54.638478 INFO::Fitting model to feature number 6, Bacteroides.caccae
2025-02-04 08:25:54.836696 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2025-02-04 08:25:55.030917 INFO::Fitting model to feature number 8, Bacteroides.dorei
2025-02-04 08:25:55.23025 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2025-02-04 08:25:55.429291 INFO::Fitting model to feature number 10, Bacteroides.faecis
2025-02-04 08:25:55.630603 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2025-02-04 08:25:55.843988 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2025-02-04 08:25:56.036343 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2025-02-04 08:25:56.202556 WARNING::Fitting problem for feature 13 a warning was issued
2025-02-04 08:25:56.419069 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2025-02-04 08:25:56.613549 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2025-02-04 08:25:56.824701 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2025-02-04 08:25:57.015771 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2025-02-04 08:25:57.218951 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2025-02-04 08:25:57.428229 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2025-02-04 08:25:57.622119 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2025-02-04 08:25:57.846194 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2025-02-04 08:25:58.050151 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2025-02-04 08:25:58.257802 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2025-02-04 08:25:58.462862 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2025-02-04 08:25:58.672015 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2025-02-04 08:25:58.871903 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2025-02-04 08:25:59.081652 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2025-02-04 08:25:59.295005 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2025-02-04 08:25:59.504782 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2025-02-04 08:25:59.724306 INFO::Fitting model to feature number 30, Paraprevotella.clara
2025-02-04 08:25:59.923294 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2025-02-04 08:26:00.129686 INFO::Fitting model to feature number 32, Prevotella.copri
2025-02-04 08:26:00.329162 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2025-02-04 08:26:00.521061 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2025-02-04 08:26:00.729792 INFO::Fitting model to feature number 35, Alistipes.putredinis
2025-02-04 08:26:00.932542 INFO::Fitting model to feature number 36, Alistipes.shahii
2025-02-04 08:26:01.151192 INFO::Fitting model to feature number 37, Alistipes.unclassified
2025-02-04 08:26:01.355088 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2025-02-04 08:26:01.563877 INFO::Fitting model to feature number 39, Clostridium.bolteae
2025-02-04 08:26:01.765004 INFO::Fitting model to feature number 40, Clostridium.citroniae
2025-02-04 08:26:01.957116 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2025-02-04 08:26:02.165229 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2025-02-04 08:26:02.359461 INFO::Fitting model to feature number 43, Clostridium.leptum
2025-02-04 08:26:02.815509 INFO::Fitting model to feature number 44, Clostridium.nexile
2025-02-04 08:26:03.020251 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2025-02-04 08:26:03.218899 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2025-02-04 08:26:03.425276 INFO::Fitting model to feature number 47, Eubacterium.eligens
2025-02-04 08:26:03.630027 INFO::Fitting model to feature number 48, Eubacterium.hallii
2025-02-04 08:26:03.826346 INFO::Fitting model to feature number 49, Eubacterium.rectale
2025-02-04 08:26:04.014728 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2025-02-04 08:26:04.20397 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2025-02-04 08:26:04.396279 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2025-02-04 08:26:04.575931 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2025-02-04 08:26:04.722627 WARNING::Fitting problem for feature 53 a warning was issued
2025-02-04 08:26:04.924084 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2025-02-04 08:26:05.112427 INFO::Fitting model to feature number 55, Ruminococcus.torques
2025-02-04 08:26:05.300813 INFO::Fitting model to feature number 56, Coprococcus.comes
2025-02-04 08:26:05.51585 INFO::Fitting model to feature number 57, Dorea.longicatena
2025-02-04 08:26:05.716571 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2025-02-04 08:26:05.922747 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2025-02-04 08:26:06.378782 INFO::Fitting model to feature number 60, Roseburia.hominis
2025-02-04 08:26:06.577563 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2025-02-04 08:26:06.774007 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2025-02-04 08:26:06.973756 INFO::Fitting model to feature number 63, Roseburia.unclassified
2025-02-04 08:26:07.214705 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2025-02-04 08:26:07.430565 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2025-02-04 08:26:07.643748 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2025-02-04 08:26:07.856202 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2025-02-04 08:26:08.038662 WARNING::Fitting problem for feature 67 a warning was issued
2025-02-04 08:26:08.246299 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2025-02-04 08:26:08.437357 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2025-02-04 08:26:08.641864 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2025-02-04 08:26:08.866724 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2025-02-04 08:26:09.067655 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2025-02-04 08:26:09.138037 WARNING::Fitting problem for feature 72 a warning was issued
2025-02-04 08:26:09.343181 INFO::Fitting model to feature number 73, Dialister.invisus
2025-02-04 08:26:09.545222 INFO::Fitting model to feature number 74, Veillonella.atypica
2025-02-04 08:26:09.760555 INFO::Fitting model to feature number 75, Veillonella.dispar
2025-02-04 08:26:09.959939 INFO::Fitting model to feature number 76, Veillonella.parvula
2025-02-04 08:26:10.166317 INFO::Fitting model to feature number 77, Veillonella.unclassified
2025-02-04 08:26:10.37398 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2025-02-04 08:26:10.573991 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2025-02-04 08:26:10.780182 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2025-02-04 08:26:10.974201 INFO::Fitting model to feature number 81, Bilophila.unclassified
2025-02-04 08:26:11.187258 INFO::Fitting model to feature number 82, Escherichia.coli
2025-02-04 08:26:11.381093 INFO::Fitting model to feature number 83, Escherichia.unclassified
2025-02-04 08:26:11.575962 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2025-02-04 08:26:11.777658 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2025-02-04 08:26:11.99754 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2025-02-04 08:26:12.208712 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2025-02-04 08:26:12.447385 INFO::Counting total values for each feature
2025-02-04 08:26:12.483026 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2025-02-04 08:26:12.59988 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2025-02-04 08:26:12.715801 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2025-02-04 08:26:12.837686 INFO::Writing residuals to file output2/fits/residuals.rds
2025-02-04 08:26:12.913476 INFO::Writing fitted values to file output2/fits/fitted.rds
2025-02-04 08:26:12.985428 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2025-02-04 08:26:12.992126 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2025-02-04 08:26:12.997905 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 42.915   1.098  44.145

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin2116.458 0.994117.758